Re: [gmx-users] how to stop duplicate atoms from being deleted
Jennifer Williams wrote: Hi Justin, Thanks for the new suggestion. However, wouldn't this again involve the sorting of my .pdb file? I have modified the specbond.dat 3 MSI SI4 MOO 2 0.16 MCM MCM MSI SI4 MOH OH2 0.16 MCM MCM MOH OH2 MHH 1 0.101 MCM MCM BUT the specbond.dat is called after the duplicate atoms are deleted: Now there are 4 atoms. Deleted 4280 duplicates. Opening library file /home/jwillia4/gromacs-4.0.5/code/share/gromacs/top/specbond.dat 3 out of 3 lines of specbond.dat converted succesfully So at present my pdb file is shortened down to 4 atoms before specdat even gets a chance to work on it. You need separate residues, and if necessary, separate names for different residue types. The only solution I can see to this is to rename each and every atom in my .pdb file with a different residue number and name. This then means that I would need a huge specbond.dat where the bonds were defined for each of these residues-this would essentially mean defining thousands of bonds as I wouldn't be able to define the bonds by atom type but by their individual reside number. Is this correct or am I missing something? You don't need a huge specbond.dat; as I see it, you only have nine possible types of residues - those around the edges, and interior ones. I will send you a test case (off-list) that worked for me. What I really would like is to stop the program deleting these duplicate atoms-then I could use pdb2gmx to generate the entire topology file. Do you know a way of doing this (and here I am really hoping that I don't have to mess with the source code :) )? Unfortunately, you cannot do this without modifying the source, and pdb2gmx is a big program that is somewhat difficult to work with. -Justin Thanks -I am learning a lot from your advice Jenny Quoting "Justin A. Lemkul" : Justin A. Lemkul wrote: I can see how this rapidly becomes difficult :) I don't believe that pdb2gmx can handle such "multi-directional" bonding, since the residues that are connected are not necessarily numerically sequential. I should amend this statement (typing quicker than the brain can keep up!) - It is not that pdb2gmx cannot handle multi-directional bonding, it is moreso that I don't think it cannot be done using the +/- convention of the .rtp files. Using specbond.dat, as I suggested before, should be a viable alternative. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Dr. Jennifer Williams Institute for Materials and Processes School of Engineering University of Edinburgh Sanderson Building The King's Buildings Mayfield Road Edinburgh, EH9 3JL, United Kingdom Phone: ++44 (0)131 650 4 861 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how to stop duplicate atoms from being deleted
Hi Justin, Thanks for the new suggestion. However, wouldn't this again involve the sorting of my .pdb file? I have modified the specbond.dat 3 MSI SI4 MOO 2 0.16 MCM MCM MSI SI4 MOH OH2 0.16 MCM MCM MOH OH2 MHH 1 0.101 MCM MCM BUT the specbond.dat is called after the duplicate atoms are deleted: Now there are 4 atoms. Deleted 4280 duplicates. Opening library file /home/jwillia4/gromacs-4.0.5/code/share/gromacs/top/specbond.dat 3 out of 3 lines of specbond.dat converted succesfully So at present my pdb file is shortened down to 4 atoms before specdat even gets a chance to work on it. The only solution I can see to this is to rename each and every atom in my .pdb file with a different residue number and name. This then means that I would need a huge specbond.dat where the bonds were defined for each of these residues-this would essentially mean defining thousands of bonds as I wouldn't be able to define the bonds by atom type but by their individual reside number. Is this correct or am I missing something? What I really would like is to stop the program deleting these duplicate atoms-then I could use pdb2gmx to generate the entire topology file. Do you know a way of doing this (and here I am really hoping that I don't have to mess with the source code :) )? Thanks -I am learning a lot from your advice Jenny Quoting "Justin A. Lemkul" : Justin A. Lemkul wrote: I can see how this rapidly becomes difficult :) I don't believe that pdb2gmx can handle such "multi-directional" bonding, since the residues that are connected are not necessarily numerically sequential. I should amend this statement (typing quicker than the brain can keep up!) - It is not that pdb2gmx cannot handle multi-directional bonding, it is moreso that I don't think it cannot be done using the +/- convention of the .rtp files. Using specbond.dat, as I suggested before, should be a viable alternative. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Dr. Jennifer Williams Institute for Materials and Processes School of Engineering University of Edinburgh Sanderson Building The King's Buildings Mayfield Road Edinburgh, EH9 3JL, United Kingdom Phone: ++44 (0)131 650 4 861 -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how to stop duplicate atoms from being deleted
Justin A. Lemkul wrote: I can see how this rapidly becomes difficult :) I don't believe that pdb2gmx can handle such "multi-directional" bonding, since the residues that are connected are not necessarily numerically sequential. I should amend this statement (typing quicker than the brain can keep up!) - It is not that pdb2gmx cannot handle multi-directional bonding, it is moreso that I don't think it cannot be done using the +/- convention of the .rtp files. Using specbond.dat, as I suggested before, should be a viable alternative. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how to stop duplicate atoms from being deleted
Jennifer Williams wrote: Thanks again for the help. I?ve given it a go but am not overly confident or exactly sure how I would translate this method to my system. This is because rather than having a chain with a well defined start and finish I have a giant covalent structure (like a web) where each silicon is tetrahedrally bound to oxygen (as in quartz). O? | ?O-Si-O ? | O? Here I describe my efforts so far. I have defined a monomer (my internal unit) as an SiO4 tetrahedra. Therefore each monomer would have to form 4 bonds with other monomers. I have defined my internal residue like this: ; Internal residue [ MCM_I ] [ atoms ] SISI1.280 1 O1O1 -0.640 1 O2O2 -0.640 1 O3O3 -0.640 1 O4O4 -0.640 1 [ bonds ] SIO1 SIO2 SIO3 SIO4 O1 -SI O2 -SI O3 +SI O4 +SI As an aside-This means that each residue is not neutral as the charges cancel out over the entire molecule and not over a single residue-I am not sure of the implications of this. To complicate matters, in my structure not all of the oxygens are bonded oxygens (i.e where each O is bonded to 2 silicons, some of the oxygens terminate in hydroxyl groups). This means that I have will have 3 types of terminal/starting chain 1. Si, O, O, OH 2. SI, O, OH, OH 3. SI, OH, OH, OH (the group which really does terminate) Here are my terminal and starting residues: ; terminal residue 1 (3OH groups) [ MCM_T1 ] [ atoms ] SISI 1.280 1 OH1OH1 -0.502 1 H1H1 0.206 1 OH2OH2 -0.502 1 H2H2 0.206 1 OH3OH3 -0.502 1 H3H3 0.206 1 O4O4-0.640 1 [ bonds ] SI OH1 SI OH2 SI OH3 SIO4 OH1 H1 OH2 H2 OH3 H3 O4 -SI ; terminal residue 2 (2 OH groups) [ MCM_T2 ] [ atoms ] SISI 1.280 1 OH1 OH1-0.502 1 H1H1 0.206 1 OH2 OH2-0.502 1 H2H2 0.206 1 O3O3-0.640 1 O4O4-0.640 1 [ bonds ] SI OH1 SI OH2 SIO3 SIO4 OH1 H1 OH2 H2 O3 -SI O4 -SI ; terminal residue 3 (1 OH group) [ MCM_T3 ] [ atoms ] SI SI 1.280 1 OH1 OH1-0.502 1 H1H1 0.206 1 O2O2-0.640 1 O3O3-0.640 1 O4O4-0.640 1 [ bonds ] SI OH1 SIO2 SIO3 SIO4 OH1H1 O2 -SI O3 -SI O4 -SI As each of these groups could equally be starting groups-I have defined them as such by changing the minus sign to a plus ; starting residue 1 [ MCM_S1 ] [ atoms ] SISI1.280 1 OH1OH1 -0.502 1 H1H1 0.206 1 OH2OH2 -0.502 1 H2H2 0.206 1 OH3OH3 -0.502 1 H3H3 0.206 1 O4O4-0.640 1 [ bonds ] SI OH1 SI OH2 SI OH3 SIO4 O4 +SI ; starting residue 2 [ MCM_T2 ] [ atoms ] SISI 1.280 1 OH1 OH1-0.502 1 H1H1 0.206 1 OH2 OH2-0.502 1 H2H2 0.206 1 O3O3-0.640 1 O4O4-0.640 1 [ bonds ] SI OH1 SI OH2 SIO3 SIO4 O3 +SI O4 +SI ; starting residue 3 [ MCM_T3 ] [ atoms ] SI SI 1.280 1 OH1 OH1-0.502 1 H1H1 0.206 1 O2O2-0.640 1 O3O3-0.640 1 O4O4-0.640 1 [ bonds ] SI OH1 SIO2 SIO3 SIO4 O2 +SI O3 +SI O4 +SI There are a few problems with this: 1.I don?t know how to go about splitting my large .pdb file into monomers. At the moment it is ordered by atomtype VMD doesn?t recognise my self- defined SiO2 tetrahedra as monomers so I can?t sort using that. There is no way I can do this manually by looking at the coordinates. 2.Looking at the terminal residue 1 for example, I have defined the only non-bonded oxygen as O4-however it could equally be O1, O2 or O3-this leads to a number of possible combinations of my terminal and internal residues. 3.There is in fact no such thing as a terminal residue (except in the case of Terminal residue 1 which is rare). It is more common to have a 2 OH groups on a silicon meaning the other oxygens bond to further residues. I can see how this method works nicely for a chain but having a four coordinate system really complicates things! I have run a very simple pdb file using pdb2gmx, the new .rtp file above and a handwritten .pdb file with 2 monomers. The result is that pdb2gmx is creating extra bonds between the Silicon of one monomer and the oxygen of the next meaning I am getting a 5-coordinate Silicon. Pdb2gmx doesn?t seem to be able to distinguish based on bond distanc
Re: [gmx-users] how to stop duplicate atoms from being deleted
Thanks again for the help. I?ve given it a go but am not overly confident or exactly sure how I would translate this method to my system. This is because rather than having a chain with a well defined start and finish I have a giant covalent structure (like a web) where each silicon is tetrahedrally bound to oxygen (as in quartz). O? | ?O-Si-O ? | O? Here I describe my efforts so far. I have defined a monomer (my internal unit) as an SiO4 tetrahedra. Therefore each monomer would have to form 4 bonds with other monomers. I have defined my internal residue like this: ; Internal residue [ MCM_I ] [ atoms ] SISI1.280 1 O1O1 -0.640 1 O2O2 -0.640 1 O3O3 -0.640 1 O4O4 -0.640 1 [ bonds ] SIO1 SIO2 SIO3 SIO4 O1 -SI O2 -SI O3 +SI O4 +SI As an aside-This means that each residue is not neutral as the charges cancel out over the entire molecule and not over a single residue-I am not sure of the implications of this. To complicate matters, in my structure not all of the oxygens are bonded oxygens (i.e where each O is bonded to 2 silicons, some of the oxygens terminate in hydroxyl groups). This means that I have will have 3 types of terminal/starting chain 1. Si, O, O, OH 2. SI, O, OH, OH 3. SI, OH, OH, OH (the group which really does terminate) Here are my terminal and starting residues: ; terminal residue 1 (3OH groups) [ MCM_T1 ] [ atoms ] SISI 1.280 1 OH1OH1 -0.502 1 H1H1 0.206 1 OH2OH2 -0.502 1 H2H2 0.206 1 OH3OH3 -0.502 1 H3H3 0.206 1 O4O4-0.640 1 [ bonds ] SI OH1 SI OH2 SI OH3 SIO4 OH1 H1 OH2 H2 OH3 H3 O4 -SI ; terminal residue 2 (2 OH groups) [ MCM_T2 ] [ atoms ] SISI 1.280 1 OH1 OH1-0.502 1 H1H1 0.206 1 OH2 OH2-0.502 1 H2H2 0.206 1 O3O3-0.640 1 O4O4-0.640 1 [ bonds ] SI OH1 SI OH2 SIO3 SIO4 OH1 H1 OH2 H2 O3 -SI O4 -SI ; terminal residue 3 (1 OH group) [ MCM_T3 ] [ atoms ] SI SI 1.280 1 OH1 OH1-0.502 1 H1H1 0.206 1 O2O2-0.640 1 O3O3-0.640 1 O4O4-0.640 1 [ bonds ] SI OH1 SIO2 SIO3 SIO4 OH1H1 O2 -SI O3 -SI O4 -SI As each of these groups could equally be starting groups-I have defined them as such by changing the minus sign to a plus ; starting residue 1 [ MCM_S1 ] [ atoms ] SISI1.280 1 OH1OH1 -0.502 1 H1H1 0.206 1 OH2OH2 -0.502 1 H2H2 0.206 1 OH3OH3 -0.502 1 H3H3 0.206 1 O4O4-0.640 1 [ bonds ] SI OH1 SI OH2 SI OH3 SIO4 O4 +SI ; starting residue 2 [ MCM_T2 ] [ atoms ] SISI 1.280 1 OH1 OH1-0.502 1 H1H1 0.206 1 OH2 OH2-0.502 1 H2H2 0.206 1 O3O3-0.640 1 O4O4-0.640 1 [ bonds ] SI OH1 SI OH2 SIO3 SIO4 O3 +SI O4 +SI ; starting residue 3 [ MCM_T3 ] [ atoms ] SI SI 1.280 1 OH1 OH1-0.502 1 H1H1 0.206 1 O2O2-0.640 1 O3O3-0.640 1 O4O4-0.640 1 [ bonds ] SI OH1 SIO2 SIO3 SIO4 O2 +SI O3 +SI O4 +SI There are a few problems with this: 1. I don?t know how to go about splitting my large .pdb file into monomers. At the moment it is ordered by atomtype VMD doesn?t recognise my self- defined SiO2 tetrahedra as monomers so I can?t sort using that. There is no way I can do this manually by looking at the coordinates. 2. Looking at the terminal residue 1 for example, I have defined the only non-bonded oxygen as O4-however it could equally be O1, O2 or O3-this leads to a number of possible combinations of my terminal and internal residues. 3. There is in fact no such thing as a terminal residue (except in the case of Terminal residue 1 which is rare). It is more common to have a 2 OH groups on a silicon meaning the other oxygens bond to further residues. I can see how this method works nicely for a chain but having a four coordinate system really complicates things! I have run a very simple pdb file using pdb2gmx, the new .rtp file above and a handwritten .pdb file with 2 monomers. The result is that pdb2gmx is creating extra bonds between the Silicon of one monomer and the oxygen of the next meaning I am getting a 5-coordinate Silicon. Pdb2gmx doesn?t seem to be able to distinguish based on bond distances whi
Re: [gmx-users] how to stop duplicate atoms from being deleted
Jennifer Williams wrote: Hi Justin, Thanks for the reply. I am in fact studying one huge molecule. All of my atoms are bonded together in one large structure (kind of like a zeolite) so I have necessarily defined them as a single residue. I would argue that you have a polymer, which can certainly be handled by pdb2gmx. See below. There is no way I can split this molecule into smaller subunits and thus define a number of residues-it wouldn't make sense to do so. If you have a lot of repetition, I would think it would be quite easy to split it apart. Yes in my .rtp file I have only defined each atom type once. To define each and every atom in my one residue would mean defining 4284 atoms! If you have a repeating structure, you have a polymer, so you can just decompose a repeat unit into a single .rtp entry. That's the entire purpose of pdb2gmx, we certainly wouldn't want to create an .rtp entry for every single possible protein either! For more information, see here: http://www.gromacs.org/Documentation/How-tos/Polymers I am having real trouble in creating topology files for my structure. At the moment, the only way I can do this is by using a tool in DL_POLY to create a field file and then manually change it to a .top file. This is really fiddely and I have a number of similar structures to do this for. I was hoping that I could do a similar step in Gromacs and get a .top file straight away-even if it means a bit more work setting it up. Is there any hope or is pdb2gmx simply not designed to work for this sort of system? You can certainly use pdb2gmx, it is intended to be versatile so it can be used with any repeating structure of monomers, homogenous (like a repeating polymer) or heterogenous (like a protein). See the link above. -Justin Thanks Jenny Quoting "Justin A. Lemkul" : Quoting Jennifer Williams : Hello I am studying a mesoporous silica for which there is no topology in gromacs-to try to automate the process of generating a topology file (x2top doesn?t work), I am using pdb2gmx (or rather trying to). I have parameters for my silica structure and have added a new section for my molecule to the .rtp file, .atp file, atommass.dat, atom_nom.dbl, nb.itp and bon.itp files. The problem is that when I use my .pdb file to generate a topology, pdb2gmx checks for duplicates and removes almost all of my atoms. It leaves only one of each type. I should have a few hundred of each atom type?here is the output from pdb2gmx? Analyzing pdb file There are 1 chains and 0 blocks of water and 1 residues with 4284 atoms chain #res #atoms 1 ' ' 1 4284 All occupancies are one All ok up to here?and then?. Processing chain 1 (4284 atoms, 1 residues) There are 552 donors and 2580 acceptors There are 1603 hydrogen bonds Checking for duplicate atoms Now there are 4 atoms. Deleted 4280 duplicates. Can anyone explain why this is happening? ?none of my atoms have the same coordinates. Is there a file that I have forgotten to alter? Is there is fix to turn off the checking of duplicate atoms? I don?t want any of my atoms to be deleted! You have all of your atoms defined within one residue. I'm assuming your .rtp entry contains the definition of a single repeat unit, so each monomer should be a separate residue. The coordinates don't matter, it's because within each residue, you have the same atom names, so pdb2gmx removes them when it finds them. Below I paste an extract of my pdb file? I'm assuming you'll have to probably reconstruct this file to re-organize the atoms to define continuous residues. It appears they are grouped by atom name, which is probably not what you want. -Justin CRYST1 46.421 43.630 75.838 90.00 90.00 120.00 P 1 1 ATOM 1 SI MCM 1 -21.090 -1.951 -29.596 1.00 0.00 SI ATOM 2 SI MCM 1 -21.090 -1.951 -10.636 1.00 0.00 SI ??.. ATOM 1153 OMCM 1 20.602 -18.404 -20.904 1.00 0.00 O ATOM 1154 OMCM 1 20.602 -18.404 -1.945 1.00 0.00 O ? ATOM 3181 OH MCM 1 -6.620 -18.769 -32.169 1.00 0.00 ATOM 3182 OH MCM 1 -6.620 -18.769 -13.210 1.00 0.00 . ATOM 3733 HMCM 1 -6.674 -18.381 -33.035 1.00 0.00 H ATOM 3734 HMCM 1 -6.616 -18.600 -14.144 1.00 0.00 H Any advice appreciated, Thanks in advance -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_list
Re: [gmx-users] how to stop duplicate atoms from being deleted
Hi Justin, Thanks for the reply. I am in fact studying one huge molecule. All of my atoms are bonded together in one large structure (kind of like a zeolite) so I have necessarily defined them as a single residue. There is no way I can split this molecule into smaller subunits and thus define a number of residues-it wouldn't make sense to do so. Yes in my .rtp file I have only defined each atom type once. To define each and every atom in my one residue would mean defining 4284 atoms! I am having real trouble in creating topology files for my structure. At the moment, the only way I can do this is by using a tool in DL_POLY to create a field file and then manually change it to a .top file. This is really fiddely and I have a number of similar structures to do this for. I was hoping that I could do a similar step in Gromacs and get a .top file straight away-even if it means a bit more work setting it up. Is there any hope or is pdb2gmx simply not designed to work for this sort of system? Thanks Jenny Quoting "Justin A. Lemkul" : Quoting Jennifer Williams : Hello I am studying a mesoporous silica for which there is no topology in gromacs-to try to automate the process of generating a topology file (x2top doesn?t work), I am using pdb2gmx (or rather trying to). I have parameters for my silica structure and have added a new section for my molecule to the .rtp file, .atp file, atommass.dat, atom_nom.dbl, nb.itp and bon.itp files. The problem is that when I use my .pdb file to generate a topology, pdb2gmx checks for duplicates and removes almost all of my atoms. It leaves only one of each type. I should have a few hundred of each atom type?here is the output from pdb2gmx? Analyzing pdb file There are 1 chains and 0 blocks of water and 1 residues with 4284 atoms chain #res #atoms 1 ' ' 1 4284 All occupancies are one All ok up to here?and then?. Processing chain 1 (4284 atoms, 1 residues) There are 552 donors and 2580 acceptors There are 1603 hydrogen bonds Checking for duplicate atoms Now there are 4 atoms. Deleted 4280 duplicates. Can anyone explain why this is happening? ?none of my atoms have the same coordinates. Is there a file that I have forgotten to alter? Is there is fix to turn off the checking of duplicate atoms? I don?t want any of my atoms to be deleted! You have all of your atoms defined within one residue. I'm assuming your .rtp entry contains the definition of a single repeat unit, so each monomer should be a separate residue. The coordinates don't matter, it's because within each residue, you have the same atom names, so pdb2gmx removes them when it finds them. Below I paste an extract of my pdb file? I'm assuming you'll have to probably reconstruct this file to re-organize the atoms to define continuous residues. It appears they are grouped by atom name, which is probably not what you want. -Justin CRYST1 46.421 43.630 75.838 90.00 90.00 120.00 P 1 1 ATOM 1 SI MCM 1 -21.090 -1.951 -29.596 1.00 0.00 SI ATOM 2 SI MCM 1 -21.090 -1.951 -10.636 1.00 0.00 SI ??.. ATOM 1153 OMCM 1 20.602 -18.404 -20.904 1.00 0.00 O ATOM 1154 OMCM 1 20.602 -18.404 -1.945 1.00 0.00 O ? ATOM 3181 OH MCM 1 -6.620 -18.769 -32.169 1.00 0.00 ATOM 3182 OH MCM 1 -6.620 -18.769 -13.210 1.00 0.00 . ATOM 3733 HMCM 1 -6.674 -18.381 -33.035 1.00 0.00 H ATOM 3734 HMCM 1 -6.616 -18.600 -14.144 1.00 0.00 H Any advice appreciated, Thanks in advance -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalem...@vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Dr. Jennifer Williams Institute for Materials and Processes School of Engine
Re: [gmx-users] how to stop duplicate atoms from being deleted
Quoting Jennifer Williams : > > Hello > > I am studying a mesoporous silica for which there is no topology in > gromacs-to try to automate the process of generating a topology file > (x2top doesn?t work), I am using pdb2gmx (or rather trying to). > > I have parameters for my silica structure and have added a new section > for my molecule to the .rtp file, .atp file, atommass.dat, > atom_nom.dbl, nb.itp and bon.itp files. > > The problem is that when I use my .pdb file to generate a topology, > pdb2gmx checks for duplicates and removes almost all of my atoms. It > leaves only one of each type. I should have a few hundred of each atom > type?here is the output from pdb2gmx? > > Analyzing pdb file > There are 1 chains and 0 blocks of water and 1 residues with 4284 atoms >chain #res #atoms >1 ' ' 1 4284 > All occupancies are one > > All ok up to here?and then?. > > Processing chain 1 (4284 atoms, 1 residues) > There are 552 donors and 2580 acceptors > There are 1603 hydrogen bonds > Checking for duplicate atoms > Now there are 4 atoms. Deleted 4280 duplicates. > > Can anyone explain why this is happening? ?none of my atoms have the > same coordinates. Is there a file that I have forgotten to alter? Is > there is fix to turn off the checking of duplicate atoms? I don?t want > any of my atoms to be deleted! You have all of your atoms defined within one residue. I'm assuming your .rtp entry contains the definition of a single repeat unit, so each monomer should be a separate residue. The coordinates don't matter, it's because within each residue, you have the same atom names, so pdb2gmx removes them when it finds them. > > Below I paste an extract of my pdb file? > I'm assuming you'll have to probably reconstruct this file to re-organize the atoms to define continuous residues. It appears they are grouped by atom name, which is probably not what you want. -Justin > CRYST1 46.421 43.630 75.838 90.00 90.00 120.00 P 1 1 > ATOM 1 SI MCM 1 -21.090 -1.951 -29.596 1.00 0.00 SI > ATOM 2 SI MCM 1 -21.090 -1.951 -10.636 1.00 0.00 SI > ??.. > ATOM 1153 OMCM 1 20.602 -18.404 -20.904 1.00 0.00 O > ATOM 1154 OMCM 1 20.602 -18.404 -1.945 1.00 0.00 O > ? > ATOM 3181 OH MCM 1 -6.620 -18.769 -32.169 1.00 0.00 > ATOM 3182 OH MCM 1 -6.620 -18.769 -13.210 1.00 0.00 > . > ATOM 3733 HMCM 1 -6.674 -18.381 -33.035 1.00 0.00 H > ATOM 3734 HMCM 1 -6.616 -18.600 -14.144 1.00 0.00 H > > Any advice appreciated, > > Thanks in advance > > > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalem...@vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] how to stop duplicate atoms from being deleted
Hello I am studying a mesoporous silica for which there is no topology in gromacs-to try to automate the process of generating a topology file (x2top doesn?t work), I am using pdb2gmx (or rather trying to). I have parameters for my silica structure and have added a new section for my molecule to the .rtp file, .atp file, atommass.dat, atom_nom.dbl, nb.itp and bon.itp files. The problem is that when I use my .pdb file to generate a topology, pdb2gmx checks for duplicates and removes almost all of my atoms. It leaves only one of each type. I should have a few hundred of each atom type?here is the output from pdb2gmx? Analyzing pdb file There are 1 chains and 0 blocks of water and 1 residues with 4284 atoms chain #res #atoms 1 ' ' 1 4284 All occupancies are one All ok up to here?and then?. Processing chain 1 (4284 atoms, 1 residues) There are 552 donors and 2580 acceptors There are 1603 hydrogen bonds Checking for duplicate atoms Now there are 4 atoms. Deleted 4280 duplicates. Can anyone explain why this is happening? ?none of my atoms have the same coordinates. Is there a file that I have forgotten to alter? Is there is fix to turn off the checking of duplicate atoms? I don?t want any of my atoms to be deleted! Below I paste an extract of my pdb file? CRYST1 46.421 43.630 75.838 90.00 90.00 120.00 P 1 1 ATOM 1 SI MCM 1 -21.090 -1.951 -29.596 1.00 0.00 SI ATOM 2 SI MCM 1 -21.090 -1.951 -10.636 1.00 0.00 SI ??.. ATOM 1153 OMCM 1 20.602 -18.404 -20.904 1.00 0.00 O ATOM 1154 OMCM 1 20.602 -18.404 -1.945 1.00 0.00 O ? ATOM 3181 OH MCM 1 -6.620 -18.769 -32.169 1.00 0.00 ATOM 3182 OH MCM 1 -6.620 -18.769 -13.210 1.00 0.00 . ATOM 3733 HMCM 1 -6.674 -18.381 -33.035 1.00 0.00 H ATOM 3734 HMCM 1 -6.616 -18.600 -14.144 1.00 0.00 H Any advice appreciated, Thanks in advance -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
